[BioC] combineAffyBatch for HG-U133A and HG-U133Av2 GeneChips

[Wolfgang Huber]

Hi Kellie


> Thanks Wolfgang. I recognize the median polish applied per probe set
> will be unaffected, but I did not want these probe sets to be included
> in the quantile normalization. I also may want to eliminate all
> control probes prior to normalization and expression summaries. I
> tried the code below and received the following message:
> 
>>rm(grep("AFFX-r2-H", gn, value=TRUE), envir=comb)

Try

   rm(list=grep("AFFX-r2-H", gn, value=TRUE), envir=comb)

but also please read the manual pages and the documentation of the affy
package on how AffyBatches are internally structured, and do some
hands-on experimentation - you're doing quite a bit of untested
under-the-hood manipulation here and you want to know what you are doing.


David:

>Umm, no matter how nominally "robust" a method, you are always better 
>off explicitly getting rid of KNOWN unwanted-signal (ie, noise) rather 
>than relying on the methodology ignoring it.  Even medians can be 
badly >perturbed by the inclusion of relatively small proportions
(10-15%) of >asymmetric (all high or all low) "non-informative signal".

Sure, you are right. It's good to see that people are following these
threads and are watchful :).

Best wishes
  Wolfgang

-- 
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http:  www.dkfz.de/abt0840/whuber
-------------------------------------


-- 
-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Http:  www.dkfz.de/abt0840/whuber